Reaction kinetics + Gillespie algorithm: Propensity function?

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Summary:

What is a propensity function? And some other questions.

Main Question or Discussion Point

I'm trying to simulate a simple series reaction stochastically using Gillespie's algorithm. I found this file:

95984733_623404015051786_185437712675766272_n.png


  1. What is this 'propensity function'? Say for example I have the simple reactions:

    A --(k1)--> R
    R--(k2)--> S

    are these 'propensity functions' the rates (a wild guess)? I mean;
    α1 = k1[A]
    α2 = k2[R],

    where [A] and [R] are the number of molecules of A and R?
  2. I am assuming that these 'rate constants' are based on the number of molecules themselves, and not the 'molarity'. I also read from an article (Stochastic chemical kinetics by Lecca) that they're supposed to be different (the rate constants based on the molarity are 'continuous' or something). How do I convert the rate constants from the molarity-based ones to the number of molecules-based ones?

  3. With regards to the updating of the numbers of reactants and products, assuming the simple reactions

    A --(k1)--> R
    R--(k2)--> S

    are taken into consideration, and that the first reaction is supposed to be occuring, am I correct to assume that I subtract one molecule A and add one molecule R?

Thank you very much.
 

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